User: Rory Stark

gravatar for Rory Stark
Rory Stark1.7k
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CRUK, Cambridge, UK
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8 hours ago
Joined:
4 years, 1 month ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Bioinformatics Analyst at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 288 results • page 1 of 29 • next >
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Answer: A: Diffbind: how to include all the samples in the heatmap while using the contrast
... Hi Amir- There's actually an easy way to do this in DiffBind, by setting the mask parameter in dba.plotHeatmap (or dba.plotPCA). There's an example on the help page for dba.heatmap using a contrast that excludes the T47D samples, but makes a plot using the differentially bound sites that include th ...
written 10 hours ago by Rory Stark1.7k
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Comment: C: DiffBind for ATAC-seq
... My understanding is that the "shift" in MACS2 is related to the modelled (or expected) fragment size (namely, half the mean fragment length). As Gord says above, extending the reads to the full fragment length (instead of using the read length) will cause single-end short reads to "overlap" features ...
written 3 days ago by Rory Stark1.7k
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Answer: A: Using Diffbind on ATAC data - adapter offset issue
... Let's consolidate discussion of this issue here: https://support.bioconductor.org/p/86594/   ...
written 3 days ago by Rory Stark1.7k
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Answer: A: Differences among phenotypes with different subgroups
... DiffBind only explicitly supports a "blocked" design, where specific samples in one group share a factor value with samples in the other group. Do the control1 and disease1 cells share something in common (as well as control2/disease2 and control3/disease3)? If so you can use the group (1, 2, or 3) ...
written 13 days ago by Rory Stark1.7k
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Answer: A: ChIPseq diffbind merging peaks
... Hi Véronique- I had a look at the data you sent me. As you say, there is very low agreement on the peak calling: > dba.overlap(prol.10,mode=DBA_OLAP_RATE) [1] 7602 47 2 0 0 0 0 0 0 As you note, this is suggestive of a non-reproducible experiment. I think I may be able ...
written 21 days ago by Rory Stark1.7k
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Answer: A: DiffBind: error with dba(sampleSheet="samples.csv")
... The peak files you are using are in bed format, with the score in the 5th column. In your sample sheet, you specified the format as "raw", which expects the score in the 4th column. So if you change the values in the last column of samples.csv from "raw" to "bed", it should work. -Rory ...
written 29 days ago by Rory Stark1.7k
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Comment: C: ChIPseq diffbind merging peaks
... Hi Veronique- No, I didn't get any email. rory.stark @ cruk.cam.ac.uk   ...
written 29 days ago by Rory Stark1.7k
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Comment: C: DiffBind MA plot
... The diagonals form when there is no signal in one sample group, but there are a concentration of overlapping reads in the other sample group. In that case there is a linear relationship between the mean concentration (mean number of reads in all samples) and fold change (essentially the mean number ...
written 4 weeks ago by Rory Stark1.7k
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Answer: A: DiffBind MA plot
... Hello Rob- Each dot in the plot represents a consensus binding site. For the X axis, "concentration" refers to the mean (normalized) number of reads across all the samples for that binding site. This is reported as a log2 value, so as you go from left to right, the overall binding affinity (read de ...
written 4 weeks ago by Rory Stark1.7k
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Answer: A: DiffBind: How to change the scatter plot colors?
... Hi Senthil- Currently there is not an official way to change the colors of the MA plots in DiffBind. I can think of two ways to get MA plots with different colors. One is to do your own plotting, and the other is to hack some un-exported variables. Suppose you want to change the color of the dots ...
written 4 weeks ago by Rory Stark1.7k

Latest awards to Rory Stark

Scholar 6 weeks ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 6 weeks ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Autobiographer 6 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 11 months ago, created an answer that has been accepted. For A: ChIPQC and/or Diffbind - retrieving normalized read counts for peaks from single
Scholar 11 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 11 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 11 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Scholar 13 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 15 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 16 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Work with GRanges objects in DiffBind
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 17 months ago, created an answer that has been accepted. For A: diffBind correlation plot
Scholar 17 months ago, created an answer that has been accepted. For A: Work with GRanges objects in DiffBind
Scholar 17 months ago, created an answer that has been accepted. For A: Clarification about the functionality of dba.count and dba.analyze
Scholar 17 months ago, created an answer that has been accepted. For A: subset of samples from dba object in DiffBind
Scholar 20 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 22 months ago, created an answer that has been accepted. For A: diffBind correlation plot
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: diffBind correlation plot
Scholar 23 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Scholar 23 months ago, created an answer that has been accepted. For A: DiffBind dba.peakset() and consensus peaks
Scholar 23 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba
Scholar 23 months ago, created an answer that has been accepted. For A: problem with characters in chromosome names in DiffBind dba

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